[AMBER] Linear peptide using non standard amino acids

From: <moitrayee.mbu.iisc.ernet.in>
Date: Fri, 22 Feb 2013 02:42:03 +0530 (IST)

Dear Amber Users,

I am trying to construct a dipeptide using gamma-amino acid. I have obtained the
parameters using the red server and I use the following script to generate the
prm top and crd files:

GVA=loadmol2 GVA.mol2
loadamberparams GVA.frcmod
gva=sequence { GVA GVA }
solvatebox gva TIP3PBOX 9.00 0.75
saveamberparm gva gva.prmtop gva.prmcrd
quit

When I use the same script for VAL, it works but with GVA, it gives TER
separated units of GVA.

For parameter generation in case of GVA, I have considered the amino acid to be
in the NH-XXXX-CO state. I am a little confused how to go about this and would
very much appreciate any help in this regard.

Best Regards,
Moitrayee


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Received on Thu Feb 21 2013 - 13:30:12 PST
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